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Submitted on June 28, 2006
Revised on August 24, 2006
Accepted on September 14, 2006

A network-based analysis of polyanion binding proteins utilizing yeast protein arrays

Nazila Salamat-Miller, Jianwen Fang, Christopher W. Seidel, Aaron M. Smalter, Yassen Assenov, Mario Albrecht, and C. Russell Middaugh

Pharmaceutical Chmistry, University of Kansas, Lawrence, KS 66047

Corresponding Author: middaugh{at}ku.edu

The high affinity of certain cellular polyanions for many proteins (PolyAnion Binding Proteins; PABPs) has been previously demonstrated. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, intra- and extra-cellular protein transport as well as intracellular organization. The purpose of the proteomic studies reported here is to seek evidence for the idea that the non-specific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate (HS), and DNA), we have identified proteins which interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We have also provided evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion/protein interactions within cells and introduces an alternative way of thinking about intracellular organization.


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